Re: ERROR: Multiple definitions of 'LangevinPiston'

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu May 14 2009 - 10:19:28 CDT

Hi Roberta,
do you really mean to be running without PME?

In general, the errors that you're seeing generally indicate that the
system is becoming unstable. This could be because PME has been turned
off, or because minimization got stuck, or some other reason. I'd
recommend starting your simulated annealing run while writing the dcd
every timestep, so that you can see what the system is doing immediately
before it crashes.
Best,
Peter

roberta.rostagno wrote:
> Dear all,
> I decided to run minimization and simulated annealing with different
> conf files. I've just finished the minimization step (100000 steps with
> minimization on command). When I run the simulated annealing the
> calculation doesn't start because of the error:
>
> ERROR: Constraint failure in RATTLE algorithm for atom 1952!
> ERROR: Constraint failure; simulation has become unstable.
>
> repeated for 30 atoms. I had a look at the structure obtained from the
> minimization but all the atoms seem ok.
>
> If I run also a little minimization (1000 steps with minimize command)
> before the simulated annealing, the calculation starts and gives be back
> the warning:
>
> bad exclusion count.
> after minimization 1000 steps, when sim ann should start, I obtain the
> same error as before and the calculation aborts.
>
> Anyone have some suggestion to solve the problem?
>
>
> conf file:
>
>
> amber yes
> parmfile M52SKIresp.prmtop
> ambercoor M52SKIresp.prmcrd
> readexclusions off
> outputname 1M52SKIrespMDsimulatedannealing
> restartName 1m52SKIrespMDsimannrest
>
> set temperature 0
> # Continuing a job from the restart files
> if {1} {
> set inputname M52SKIMDsimann
> binCoordinates 1m52SKIrespsimannrest.coor
> binVelocities 1m52SKIrespsimannrest.vel ;# remove the
> "temperature" entry
> if you use this!
> extendedSystem 1m52SKIrespsimannrest.xsc
> }
>
> firsttimestep 20000
> # NOTE: Do not set the initial velocity temperature if you
> # have also specified a .vel restart file!
> #temperature $temperature
> # Periodic Boundary conditions
> # NOTE: Do not set the periodic cell basis if you have also
> # specified an .xsc restart file!
> #if {0} {
> #cellBasisVector1 88. 0. 0.
> #cellBasisVector2 0. 88 0.
> #cellBasisVector3 0. 0 88.
> #cellOrigin -0.00 -0.16 0.26
> #}
> wrapAll on
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 0.833333
> cutoff 12.
> switching on
> switchdist 10.
> pairlistdist 14.0
> # Integrator Parameters
> timestep 1;# 1 fs/step
> #numsteps 11802000
> rigidBonds all ;# needed for 2fs steps
> rigidTolerance 0.0005
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 10
> #PME (for full-system periodic electrostatics)
> if {0} {
> PME yes
> PMEGridSizeX 90
> PMEGridSizeY 90
> PMEGridSizeZ 90
> }
> # Constant Temperature Control
> langevin on ;# do langevin dynamics
> langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
> langevinTemp $temperature
> langevinHydrogen no ;# don't couple langevin bath to hydrogens
> # Constant Pressure Control (variable volume)
> if {0} {
> useGroupPressure yes ;# needed for 2fs steps
> useFlexibleCell no ;# no for water box, yes for membrane
> useConstantArea no ;# no for water box, yes for membrane
>
> langevinPiston on
> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
> langevinPistonPeriod 200.
> langevinPistonDecay 100
> langevinPistonTemp $temperature
> }
> restartfreq 200 ;# 500steps = every 1ps
> dcdfreq 100
> outputEnergies 100
> outputPressure 100
> dcdfile 1m52SKIrespMDsimann.dcd
>
> constraints on
> consRef restrain.pdb
> consKFile restrain.pdb
> consKCol B
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
> reassignFreq 1000
> #reassignTemp 0
> minimize 1000
> for { set TEMP 0 } {$TEMP<601} {incr TEMP 1} {
> reassignTemp $TEMP
> run 1000
> }
> run 500000
> for { set TEMP 600 } {$TEMP>=300} {incr TEMP -1} {
> reassignTemp $TEMP
> run 1000
> }
> run 500000
> run 4000000
>
> reassignFreq 1000
> #reassignTemp 0
> minimize 1000
> for { set TEMP 0 } {$TEMP<601} {incr TEMP 1} {
> reassignTemp $TEMP
> run 1000
> }
> run 500000
> for { set TEMP 600 } {$TEMP>=300} {incr TEMP -1} {
> reassignTemp $TEMP
> run 1000
> }
> run 500000
> run 4000000
>
> regards
>
> Roberta Rostagno
>
>
> On Tue, 12 May 2009 06:41:29 -0500
> Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
>> Hi Roberta,
>> could you include a little more context, say, up through
>>the first "run"
>> statement that you think should be doing dynamics? From
>>what I see here,
>> it looks like in the first case you're not doing any
>>minimization at all
>> due to the if statement, which would certainly explain a
>>bad global
>> exclusion count (or several other errors that boil down
>>to starting
>> dynamics from a badly strained conformation).
>> Peter
>>
>> roberta.rostagno wrote:
>>> Hi Peter,
>>>
>>> This is the config file with minimize:
>>> #############################################################
>>> ## EXECUTION SCRIPT
>>> ##
>>> #############################################################
>>>
>>> #Minimization
>>> if {0} {
>>> minimize 10000
>>> reinitvels $temperature
>>> }
>>> and this is the config file with minimization on
>>>command:
>>>
>>> minimization on
>>> if {0} {
>>> minimize 20000
>>> reinitvels $temperature
>>> }
>>> I would like to run MD with periodic boundary conditions
>>>and PME. If I
>>> use restart files the boundary conditions are read by
>>>the .xsc file? SO
>>> I can omit periodic boundary conditions information but
>>>I have to
>>> specify PME information in the config file?
>>>
>>> thanks
>>>
>>> Roberta
>>>
>>> On Mon, 11 May 2009 12:11:57 -0500
>>> Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
>>>> Hi Roberta,
>>>>
>>>> roberta.rostagno wrote:
>>>>> Thank you for your answer. If I don't use minimization
>>>>>on, but only
>>>>> minimize command after few steps I have the error:
>>>>> bad global exclusion clount. Instead with minimization
>>>>> on the
>>>>> minimization run without errors until the end.
>>>>
>>>> I can't think of any reason for minimize n and
>>>>minimization on; run n to
>>>> yield different results... could you send me snippets of
>>>>the end of the
>>>> relevant config files?
>>>>
>>>> Bad global exclusion count errors generally indicate an
>>>>overly long bond
>>>> in the system... can you visually inspect your structure
>>>>and make sure
>>>> it looks ok?
>>>>
>>>> By the way, is namd terminating upon the exclusion count
>>>>error? During
>>>> minimization, bad global exclusion counts should give a
>>>>warning but not
>>>> an error.
>>>>
>>>>> if I run minimization and MD with different conf file,
>>>>>can I use restart
>>>>> coordinate and velocity files obtained from minimization
>>>>>to start MD?
>>>>> thanks again for help
>>>>
>>>> Yes; you can read the coordinates, velocities, and
>>>>extended system from
>>>> the previous run with bincoordinates, binvelocities, and
>>>>extendedSystem,
>>>> respectively (they'll be named
>>>>$outputname.restart.coor/vel/xsc)
>>>>
>>>> By the way, are you sure you mean to be running without
>>>>pme?
>>>> Also, that rigid bond tolerance is quite large...
>>>>
>>>> Best,
>>>> Peter
>>>>
>>>
>>
>

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